Protein conformational changes are at the heart of many essential biological processes, but capturing the motion between two known conformations can be challenging—especially when you need to analyze or reuse specific atom trajectories for downstream tasks like simulation analysis, machine learning input preparation, or structural comparison.
If you’ve ever found yourself wishing for a convenient way to extract the motion of only a subset of atoms along a transition path, SAMSON’s Protein Path Finder offers a useful solution. In this post, we’ll walk through how to do this using the Export Along Paths app, giving you fine-grained control over the data you export from computed conformational pathways.
Why Export Specific Atom Trajectories?
Researchers may not always need the full protein trajectory. In practice, you might only care about the positions of catalytic residues, binding site atoms, or atoms within a domain of interest. This focused data export helps:
- Reduce file sizes and processing time.
- Facilitate focused simulation or analysis.
- Simplify data inputs for training machine learning models.
What You Need
Before you begin, make sure you have:
- Computed a path between two conformations using the Protein Path Finder app in SAMSON.
- Identified the atoms you want to track along the path.
- Installed the Export Along Paths app from SAMSON Connect.
How to Export Selected Atom Trajectories
Once you’ve computed paths, follow these steps:
- Select the path(s) of interest from the Results tab of the Protein Path Finder.
- Launch the Export Along Paths app.
- Specify which atoms to export. This can be done by selecting atoms in the Document view or using the Node Specification Language (NSL) if you prefer precise criteria.
- Set the output format and destination file. Choose whether to export individual PDB files, a .samx file, or another appropriate format.
- Click Export.
This process creates accurate trajectory data for the selected atoms efficiently—no need to work with the entire structure unless necessary.
Tips to Get the Most Out of Your Export
- You can adjust the export interval to reduce the number of conformations exported (e.g., export every 2nd or 5th frame).
- Use descriptive file names to differentiate between different subsets or paths.
- The exported files are compatible with common tools for structural analysis or visualization.
This targeted export capability aligns with workflows where precision and data handling efficiency are key. Whether you’re preparing input for another simulation or analyzing motion in a specific site, extracting only the data you need makes life simpler.
To see the full set of instructions and related tools, consult the complete Protein Path Finder tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.